PDB-5opf: Structure of LPMO10B from from Micromonospora aurantiaca

ID or keywords:

Entry

Database: PDB / ID: 5opf

Title

Structure of LPMO10B from from Micromonospora aurantiaca

Components

Chitin-binding domain 3 protein

Keywords

CARBOHYDRATE / Lytic polysaccharide monooxygenase (LPMO)

Function / homology

Function and homology information

polysaccharide binding / hydrolase activity, hydrolyzing O-glycosyl compounds / carbohydrate metabolic process
Similarity search - Function

Biological species

Micromonospora aurantiaca ATCC 27029 (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.081 Å

Authors

Forsberg, Z. / Bissaro, B. / Gullesen, J. / Dalhus, B. / Vaaje-Kolstad, G. / Eijsink, V.G.H.

Funding support

Norway,

France, 5items

Organization	Grant number	Country
Research Council of Norway	214138, 214613 and 226247	Norway
South-Eastern Norway Regional Health Authority	2015095	Norway
French Institut National de la Recherche Agronomique		France
Norwegian Academy of Science and Letters	6510	Norway
Marie-Curie FP7 COFUND People Programme	267196

Citation

Journal: J. Biol. Chem. / Year: 2018
Title: Structural determinants of bacterial lytic polysaccharide monooxygenase functionality.
Authors: Forsberg, Z. / Bissaro, B. / Gullesen, J. / Dalhus, B. / Vaaje-Kolstad, G. / Eijsink, V.G.H.

History

Deposition	Aug 9, 2017	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Dec 13, 2017	Provider: repository / Type: Initial release
Revision 1.1	Dec 20, 2017	Group: Database references / Category: citation Item: _citation.journal_abbrev / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2	Jan 24, 2018	Group: Source and taxonomy / Category: entity_src_gen Item: _entity_src_gen.pdbx_host_org_ncbi_taxonomy_id / _entity_src_gen.pdbx_host_org_scientific_name / _entity_src_gen.pdbx_host_org_strain
Revision 1.3	Feb 7, 2018	Group: Database references / Category: citation Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year
Revision 1.4	Jan 17, 2024	Group: Data collection / Database references / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	5opf.cif.gz	126.6 KB	Display	PDBx/mmCIF format
PDB format	pdb5opf.ent.gz	98.4 KB	Display	PDB format
PDBx/mmJSON format	5opf.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	5opf_validation.pdf.gz	404.7 KB	Display	wwPDB validaton report
Full document	5opf_full_validation.pdf.gz	404.7 KB	Display
Data in XML	5opf_validation.xml.gz	12.3 KB	Display
Data in CIF	5opf_validation.cif.gz	18.8 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/op/5opf ftp://data.pdbj.org/pub/pdb/validation_reports/op/5opf	HTTPS FTP

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Related structure data

Related structure data	4oy6S S: Starting model for refinement
Similar structure data	5eim-1 1z6x-1 6ndq-1 5uvq-d 1ctx-1 3tth-5 3bpj-1 3r7g-d 4m6a-5 Search similar-shape structures by Omokage search (details) Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#141 - Sep 2011 O-GlcNAc Transferase similarity (1)

Deposited unit

A: Chitin-binding domain 3 protein

hetero molecules

21.6 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

Idetical with deposited unit
defined by author&software

Unit cell

Length a, b, c (Å)	43.859, 55.088, 75.106
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	19
Space group name H-M	P2₁2₁2₁

#1: Protein	Chitin-binding domain 3 protein Mass: 21578.750 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Micromonospora aurantiaca ATCC 27029 (bacteria) Strain: ATCC 27029 / DSM 43813 / BCRC 12538 / CBS 129.76 / JCM 10878 / NBRC 16125 / NRRL B-16091 / INA 9442 Gene: Micau_1630 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: D9SZQ3
#2: Chemical	ChemComp-CU / COPPER (II) ION Mass: 63.546 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cu
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 325 / Source method: isolated from a natural source / Formula: H₂O

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Experiment

Experiment	Method: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

Crystal	Density Matthews: 2.1 Å³/Da / Density % sol: 41.49 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, hanging drop Details: 0.04 M potassium phosphate monobasic and 16 % w/v PEG8000 and 20 % v/v glycerol at a protein concentration of 21.9 mg/mL

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.8726 Å
Detector	Type: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Dec 2, 2015
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.8726 Å / Relative weight: 1
Reflection	Resolution: 1.08→44.42 Å / Num. obs: 78485 / % possible obs: 99.8 % / Redundancy: 4.8 % / R_sym value: 0.08 / Net I/σ(I): 11.5
Reflection shell	Resolution: 1.08→1.12 Å / Redundancy: 4 % / Mean I/σ(I) obs: 1.5 / Num. unique obs: 7545 / R_sym value: 0.85 / % possible all: 99.1

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Processing

Software

Name	Version	Classification
PHENIX	(1.10.1_2155: ???)	refinement
XDS		data reduction
Aimless		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 4oy6

4oy6

Resolution: 1.081→44.42 Å / SU ML: 0.09 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 13.91

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.1516	3946	5.03 %	Random selection
R_work	0.1402	-	-	-
obs	0.1408	78405	99.82 %	-

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å

Refinement step

Cycle: LAST / Resolution: 1.081→44.42 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	1524	0	1	325	1850

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.006	1604
X-RAY DIFFRACTION	f_angle_d	0.921	2207
X-RAY DIFFRACTION	f_dihedral_angle_d	12.377	570
X-RAY DIFFRACTION	f_chiral_restr	0.079	223
X-RAY DIFFRACTION	f_plane_restr	0.007	294

LS refinement shell

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Refine-ID	% reflection obs (%)
1.0807-1.0939	0.2819	154	0.2815	2560	X-RAY DIFFRACTION	98
1.0939-1.1077	0.2341	133	0.2452	2603	X-RAY DIFFRACTION	100
1.1077-1.1223	0.2311	155	0.2122	2641	X-RAY DIFFRACTION	100
1.1223-1.1377	0.2146	120	0.1962	2603	X-RAY DIFFRACTION	100
1.1377-1.1539	0.1948	139	0.1899	2657	X-RAY DIFFRACTION	100
1.1539-1.1711	0.2063	125	0.1894	2628	X-RAY DIFFRACTION	100
1.1711-1.1894	0.1931	138	0.1851	2636	X-RAY DIFFRACTION	100
1.1894-1.209	0.2079	148	0.1805	2627	X-RAY DIFFRACTION	100
1.209-1.2298	0.1923	132	0.1733	2640	X-RAY DIFFRACTION	100
1.2298-1.2522	0.1858	135	0.1746	2658	X-RAY DIFFRACTION	100
1.2522-1.2762	0.1589	148	0.1667	2621	X-RAY DIFFRACTION	100
1.2762-1.3023	0.1821	121	0.1575	2650	X-RAY DIFFRACTION	100
1.3023-1.3306	0.1702	136	0.1561	2665	X-RAY DIFFRACTION	100
1.3306-1.3616	0.1573	132	0.1442	2646	X-RAY DIFFRACTION	100
1.3616-1.3956	0.1717	147	0.1402	2617	X-RAY DIFFRACTION	100
1.3956-1.4334	0.1367	140	0.1376	2650	X-RAY DIFFRACTION	100
1.4334-1.4755	0.1453	138	0.1328	2670	X-RAY DIFFRACTION	100
1.4755-1.5232	0.1348	126	0.1258	2673	X-RAY DIFFRACTION	100
1.5232-1.5776	0.1351	144	0.1256	2655	X-RAY DIFFRACTION	100
1.5776-1.6408	0.1309	160	0.1212	2642	X-RAY DIFFRACTION	100
1.6408-1.7155	0.1144	150	0.1217	2656	X-RAY DIFFRACTION	100
1.7155-1.8059	0.154	135	0.1228	2685	X-RAY DIFFRACTION	100
1.8059-1.9191	0.1304	138	0.1218	2670	X-RAY DIFFRACTION	100
1.9191-2.0672	0.1281	145	0.1181	2696	X-RAY DIFFRACTION	100
2.0672-2.2752	0.1147	134	0.1156	2708	X-RAY DIFFRACTION	100
2.2752-2.6044	0.1415	144	0.128	2712	X-RAY DIFFRACTION	100
2.6044-3.2812	0.1574	172	0.1302	2711	X-RAY DIFFRACTION	100
3.2812-44.4579	0.1415	157	0.1359	2879	X-RAY DIFFRACTION	100

Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

ID	L11 (°²)	L12 (°²)	L13 (°²)	L22 (°²)	L23 (°²)	L33 (°²)	S11 (Å °)	S12 (Å °)	S13 (Å °)	S21 (Å °)	S22 (Å °)	S23 (Å °)	S31 (Å °)	S32 (Å °)	S33 (Å °)	T11 (Å²)	T12 (Å²)	T13 (Å²)	T22 (Å²)	T23 (Å²)	T33 (Å²)	Origin x (Å)	Origin y (Å)	Origin z (Å)
1	0.9062	-0.1515	0.3831	0.2249	-0.0082	0.4826	-0.0241	0.0684	0.0723	-0.0277	-0.0075	-0.0754	-0.0738	0.0603	0.0357	0.074	-0.0035	0.0037	0.0656	0.0082	0.0864	19.8177	29.1278	17.0518
2	0.8912	0.1356	0.2988	0.434	0.0438	1.204	0.0087	0.0579	-0.0813	-0.032	0.0189	-0.0999	0.0703	0.1633	-0.0276	0.0646	0.0136	0.0082	0.0585	-0.0058	0.0864	22.0558	20.9679	14.9399
3	0.7439	0.0355	-0.0794	0.8824	0.1628	0.7026	-0.0003	-0.0002	-0.0667	-0.0397	0.0013	-0.0648	0.02	0.0371	-0.0005	0.0628	0.0063	0.0027	0.0558	0.0087	0.0752	15.8971	17.8128	18.9922
4	0.5304	0.2816	-0.3448	0.7778	-0.1286	3.4503	-0.003	-0.0197	0.0507	0.0844	0.0206	0.0126	-0.2013	-0.0491	-0.0217	0.0912	0.0148	-0.0029	0.0645	0.0062	0.0683	7.4638	32.6279	13.4898
5	0.6967	0.0688	0.3298	0.5047	-0.0942	1.4905	0.0444	-0.0104	-0.0875	0.0305	-0.004	-0.0231	0.1169	-0.0007	-0.0507	0.0643	-0.0024	-0.0006	0.0599	-0.0013	0.0741	6.8977	18.4128	23.8181
6	1.0703	-0.2245	-0.3634	2.2002	0.0701	1.098	0.0333	0.0305	-0.0318	-0.0745	-0.0548	0.1078	-0.0334	-0.2397	0.0119	0.0533	0.0068	0.001	0.0782	-0.0072	0.0566	1.1632	19.672	22.0895
7	4.622	1.1446	0.7171	3.4376	0.5869	2.4816	-0.1724	0.1744	0.468	-0.2699	0.0775	-0.0196	-0.3594	0.0049	0.0788	0.1361	0.0191	-0.012	0.0972	0.0195	0.1145	4.0285	37.3544	7.3562
8	0.453	0.003	0.2068	0.3679	-0.3014	1.0239	0.0045	-0.0111	0.015	-0.0053	0.0192	-0.0025	-0.0373	-0.0997	-0.0235	0.0584	0.0027	0.003	0.0613	0.0002	0.0639	6.9846	25.4934	18.6892

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 37 through 57 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 58 through 99 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 100 through 132 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 132 through 145 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 146 through 166 )
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 167 through 176 )
7	X-RAY DIFFRACTION	7	chain 'A' and (resid 176 through 189 )
8	X-RAY DIFFRACTION	8	chain 'A' and (resid 190 through 230 )

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